liftOver {rtracklayer} | R Documentation |
A reimplementation of the UCSC liftover tool for lifting features from one genome build to another. In our preliminary tests, it is significantly faster than the command line tool. Like the UCSC tool, a chain file is required input.
liftOver(x, chain, ...)
x |
The intervals to lift-over, usually
a |
chain |
A |
... |
Arguments for methods. |
A GRanges
object, with intervals mapped through the chain.
Michael Lawrence
http://genome.ucsc.edu/cgi-bin/hgLiftOver
## Not run: chain <- import.chain("hg19ToHg18.over.chain") library(TxDb.Hsapiens.UCSC.hg19.knownGene) tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene) tx_hg18 <- liftOver(tx_hg19, chain) ## End(Not run)